#' CoGAPS: Coordinated Gene Activity in Pattern Sets
#'
#' CoGAPS implements a Bayesian MCMC matrix factorization algorithm,
#' GAPS, and links it to gene set statistic methods to infer
#' biological process activity.  It can be used to perform
#' sparse matrix factorization on any data, and when this
#' data represents biomolecules, to do gene set analysis.
#' \tabular{ll}{
#' Package: \tab CoGAPS\cr
#' Type: \tab Package\cr
#' Version: \tab 2.99.0\cr
#' Date: \tab 2018-01-24\cr
#' License: \tab LGPL\cr
#' }
#' @author Maintainer: Elana J. Fertig \email{ejfertig@jhmi.edu},
#'             Michael F. Ochs \email{ochsm@tcnj.edu}
#' @references
#' Fertig EJ, Ding J, Favorov AV, Parmigiani G, Ochs MF.
#' CoGAPS: an R/C++ package to identify patterns and biological
#' process activity in transcriptomic data.
#' Bioinformatics. 2010 Nov 1;26(21):2792-3
#' @docType package
#' @name CoGAPS-package
#' @importFrom Rcpp evalCpp
#' @useDynLib CoGAPS
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#' Simulated data
#' @docType data
#' @name SimpSim.data
#' @usage SimpSim.data
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#' CoGAPS result from running on simulated data
#' @docType data
#' @name SimpSim.result
#' @usage SimpSim.result
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#' GIST gene expression data from Ochs et al. (2009)
#' @docType data
#' @name GIST.data_frame
#' @usage GIST.data_frame
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#' GIST gene expression data from Ochs et al. (2009)
#' @docType data
#' @name GIST.matrix
#' @usage GIST.matrix
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#' GIST gene expression uncertainty matrix from Ochs et al. (2009)
#' @docType data
#' @name GIST.uncertainty
#' @usage GIST.uncertainty
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#' CoGAPS result from running on GIST dataset
#' @docType data
#' @name GIST.result
#' @usage GIST.result
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#' Gene sets defined by transcription factors defined from TRANSFAC.
#' @docType data
#' @name tf2ugFC
#' @usage tf2ugFC
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